title: Enhanced exchange algorithm without detailed balance condition for replica exchange method.
abstract: The replica exchange method (REM) is a powerful tool for the conformational sampling of biomolecules. In this study, we propose an enhanced exchange algorithm for REM not meeting the detailed balance condition (DBC), but satisfying the balance condition in all considered exchanges between two replicas. Breaking the DBC can minimize the rejection rate and make an exchange process rejection-free as the number of replicas increases. To enhance the efficiency of REM, all possible pairs--not only the nearest neighbor--were considered in the exchange process. The test simulations of the alanine dipeptide confirmed the correctness of our method. The average traveling distance of each replica in the temperature distribution was also increased in proportion to an increase in the exchange rate. Furthermore, we applied our algorithm to the conformational sampling of the 10-residue miniprotein, chignolin, with an implicit solvent model. The results showed a faster convergence in the calculation of its free energy landscape, compared to that achieved using the normal exchange method of adjacent pairs. This algorithm can also be applied to the conventional near neighbor method and is expected to reduce the required number of replicas.
authors.affiliation: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. h_kondo@gsc.riken.jp
authors.forename: Hiroko X
authors.initials: HX
authors.lastname: Kondo
authors.forename: Makoto
authors.initials: M
authors.lastname: Taiji
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D009842:Oligopeptides; C506175:chignolin; D000409:Alanine